De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo throu...

Full description

Bibliographic Details
Main Authors:	Liang, Mei, Yang, Xiaoming, Li, Hang, Su, Shiying, Yi, Hualin, Chai, Lijun, Deng, Xiuxin
Format:	Online
Language:	English
Published:	Public Library of Science 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370633/

id	pubmed-4370633
recordtype	oai_dc
spelling	pubmed-43706332015-04-04 De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development Liang, Mei Yang, Xiaoming Li, Hang Su, Shiying Yi, Hualin Chai, Lijun Deng, Xiuxin Research Article Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo. Public Library of Science 2015-03-23 /pmc/articles/PMC4370633/ /pubmed/25799271 http://dx.doi.org/10.1371/journal.pone.0120615 Text en © 2015 Liang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Liang, Mei Yang, Xiaoming Li, Hang Su, Shiying Yi, Hualin Chai, Lijun Deng, Xiuxin
spellingShingle	Liang, Mei Yang, Xiaoming Li, Hang Su, Shiying Yi, Hualin Chai, Lijun Deng, Xiuxin De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development
author_facet	Liang, Mei Yang, Xiaoming Li, Hang Su, Shiying Yi, Hualin Chai, Lijun Deng, Xiuxin
author_sort	Liang, Mei
title	De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development
title_short	De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development
title_full	De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development
title_fullStr	De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development
title_full_unstemmed	De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development
title_sort	de novo transcriptome assembly of pummelo and molecular marker development
description	Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo.
publisher	Public Library of Science
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370633/
_version_	1613202414378156032

De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

Similar Items